AFNI HISTORY

The levels of importance go from 1 to 5, with meanings:
       1 - users would not care
       2 - of little importance, though some users might care
       3 - fairly important
       4 - a big change or new program
       5 - IMPORTANT: we expect users to know

generated via the command : afni_history -html -reverse -type NEW_OPT 

  ----  log of AFNI updates (most recent first)  ----

23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
    added -base1_dset option, where -base1 value can vary over voxels

    Added for M Beauchamp.


16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
    added -disp_all to give formatted display of 'all' mask data

    This was added for P Kundu.

16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
    added choice of 'Vals to Send' to serial_helper

    Can now send index,i,j,k,x,y,z,value for every value in mask.


14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
    added -sleep_init, -sleep_vol, -sleep_frac

    These options control the timeout periods between data checks.


30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -gen_epi_review and -no_epi_review options

    By default, a drive_afni script to review EPI data is now generated.


25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
    added -past_entries option


13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
    added nifti_compiled_with_zlib()

13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
    added -with_zlib, and ability to add extensions via 'file:FILENAME'

    extension update added for J. Gunter


12 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
    added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D

    also, updated find_last_space to deal with long strings


10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
    Add -ARMA option to estimate ARMA(1,1) parameters


21 May 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT)
    added -amplitudes option (for Rutvik Desai)


20 May 2008, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT)
    Make TCP/IP to 'localhost' the default.  Add option '-shm' if needed.


18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
    added options for TR-locking and storing '3dDeconvolve -nodata' examples

    - added shuffle() to replace that from random (cannot produce all perms)
    - added options -tr, -tr_locked and -save_3dd_cmd
    - changed -stim_time option to -stim_dur


15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
    added -n_rand and -n_randseed


13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
    added -set_extern_filelist option, and help for using external data files

13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
    gifticlib-1.0.0: initial release

    includes support for (set/clear/read/write) external data files


09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
    Added option -1Dformat to output results in 1D format


07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
    added get_type_list and other accessor functions


28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
    added -copy_gifti_meta and -copy_DA_meta options

28 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 2 (NEW_OPT)
    added routines to copy MetaData


26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
    Added -align_centers as an option to deal with very large moves

    It used to be that users had to run @Align_Centers on all their
    data when big moves were needed to align the surface's antaomy
    to that of the experiment. This is no longer needed.

26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
    Add -norm2 and -normx options: normalize time series before plotting


25 Mar 2008, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
    Added option -ixmat_1D to apply inverse of affine transform


24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
    added GERT_Reco options (request of D Glen)

      -gert_filename    : specify a name for the GERT_Reco script
      -gert_nz          : override nz=1 in mosaic image files
      -gert_to3d_prefix : specify a dataset prefix for the to3d command


21 Mar 2008, ZS Saad, 3dnvals, level 1 (MICRO), type 2 (NEW_OPT)
    Added -all to 3dnvals to output all 4 dimensions. 


20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
    Add -polort option, to keep Gang Chen happy.


18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
    added -compare_gifti option

    See 'gifti_tool -help' for details, including example #7.

18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
    added comparison functions to gifticlib


17 Mar 2008, ZS Saad, lpc_align.py, level 1 (MICRO), type 2 (NEW_OPT)
    Added -big_move and -partial_coverage.

    -big_move is for when large displacements are needed for alignment.
    -partial_coverage is for when EPI covers a portion of the brain.


14 Mar 2008, RW Cox, 3dROIstats, level 1 (MICRO), type 2 (NEW_OPT)
    Sub-brick label printing (and -nobriklab option)

    Per the noble Vince Hradil.


11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
    added control of hematocrit via AFNI_MODEL_D3_HCT


10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
    applied -gert_outdir in the case of dicom images


07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
    Color map in surface controller can be flipped and rotated

    * f key for flipping colormap
    * Up/Down keys for rotating color map
    * Home for home
    Hit ctrl+h on Surface Controller's colormap for more help.


05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
    added '-fitts' option to produce fitted time series dataset


04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
    added -accumulate option, to output each partial sum

    for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k


03 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 2 (NEW_OPT)
    Small changes to make onscreen wordwrap match printout wordwrap


29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
    added a TYPE, -type, a new level, and a string to identify each level


28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
    allow constraints on sign of deconvolved function

28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
    allow combination of penalty functions in deconvolution

28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
    added -list_authors option and adjusted spacing


27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
    add deconvolution via the '-FALTUNG' option

    Unlike 3dDeconvolve, this deconvolution is to find the input time
    series, given the impulse response function.


25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
    add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc


22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
    add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file

    '-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
    '-reduce n pp' outputs a reduced dataset, using only the largest 'n'
    eigenvalues.


20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
    add '-1D:' option, to write output that is usable on the command line

    Sample usage:
     1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
    The backquotes `...` capture command's output and put this string on
    the command line.  The '-1D:' option formats the 1deval output so that
    it is ready to be used in this way.


12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
    An option to show all of suma's environment variables

    See help for -environment in suma -help.


31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.


24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
    * Fix little problems with AFNI threshold scale display as q-value alters.
    * Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks.
    * Add '-killSTAT' option to 3drefit.


23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * FDR thresh-vs-z(q) curve generation and storage in datasets.
    * Display FDR q in AFNI pval label.
    * Generate FDR curves automatically in 3dDeconvolve, and with
       '-addFDR' option in 3drefit.


22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added options to estimate smoothness in data for use in AlphaSim

    See help options -regress_est_blur_epits and -regress_est_blur_errts.


17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
    * mri_fdrize.c function for FDR-z conversion.


20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * Clusterize reporting window.


06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Add -jpg and -png options to 1dplot.c.
    * Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).


16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c
    * For ragged 1D input files, arbitrary text starting with alphabetic
       character is same as '*' for filler.
    * AFNI_RESCAN_AT_SWITCH is on by default now.
    * 1dplot takes a 1 row file and flips it to a column for plotting; however
    ,
       when 2 single row files were input, they'd be catenated and THEN
       flipped, producing erroneous joined plot.  Now, they are flipped
       THEN catenated, which does the right thing.
    * Speaking of 1dplot, '-nopush' now works for multiple graphs, rather
       than just for '-one'.
    * Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors,
       and so that '-seed 0' generates a custom seed.
    * Add some extra text to the 'Clusterize' label (afni_setup.c) to
       explain that rmm=0 means NN clustering with vmul in voxel count.


12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Changes to bbox.c to add an arrowval index selector to the single-select
    ion
       mode strlist chooser (per Shruti Japee's unreasonable demand).


11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Modify edt_filtervol.c to clip off voxels outside the fmask.
    * Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.


10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option;
       '-autoweight' now the default for '-ls' cost function.
    * Re-insert older fixes to afni.c that were lost in CVS.


20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * First version of '-lpc' Local Pearson Correlation cost function in
       3dAllineate.c, with rhombic dodecahedra as the default building bloks.


14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20.
    * Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti
    c.


08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).


31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
    Older History stuff

    * Make -cmass the default in 3dAllineate.c.
    * Also add '+clip' feature to '-autoweight' in 3dAllineate.c.


15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
    High resolution image saving with ctrl+r

    Very high resolution images can be created.
    See suma's interactive help 'ctrl+h' for more info.


01 Dec 2005, G Chen, 3dANOVA3, level 3 (MAJOR), type 2 (NEW_OPT)
    New options were made to run 2nd-order general linear contrasts in 3dANOVA3. 

    See more details on: http://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html


15 Jan 2003, RC Reynolds, Imon, level 3 (MAJOR), type 2 (NEW_OPT)
    added connection to the realtime plugin in afni